Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Prostate
Cell type
VCaP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
VCaP cells
cell line
VCaP
treatment1
control (37 degree C)
chip antibody
anti-Pol2, clone: 8WG16 (Covance, catalog# MMS-126R, lot# E12CF00481)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei from approximately 10 million formaldehyde crosslinked (1%; 10min at room temperature for VCaP cells, and 8min. at room temperature for K562 cells) cells were isolated and chromatin was fragmented using sonicator (bioruptor). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and protein-A/G magnetic beads. DNA fragments were purified and libraries were prepared accorcing to standard Illumina protocol. Samples were sequenced at BGI Tech Solutions (Shenzhen, China) or at the Gene Core in EMBL (Heidelberg, Germany).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
29874311
Reads aligned (%)
98.5
Duplicates removed (%)
9.4
Number of peaks
19006 (qval < 1E-05)

hg19

Number of total reads
29874311
Reads aligned (%)
97.9
Duplicates removed (%)
10.7
Number of peaks
18919 (qval < 1E-05)

Base call quality data from DBCLS SRA